Transient pressure testing is often accompanied by shock acceleration. Aiming at the acceleration-induced effects of pressure sensors, a dynamic compensation method combining empirical mode decomposition (EMD) with system identification theory (SIT) is proposed in this paper. This method is more effective at reducing the error of the acceleration-induced effects without affecting the sensor’s sensitivity and inherent frequency. The principle and theoretical basis of acceleration-induced effects is analyzed, and the static and dynamic acceleration-induced effects on the quartz crystal of a piezoelectric pressure sensor are performed. An acceleration-induced effects dynamic calibration system is built using a Machete hammer, which generates acceleration signals with larger amplitude and narrower pulse width, and an autoregressive exogenous (ARX)mathematical model of acceleration-induced effects is obtained using empirical mode decomposition-system identification theory (EMD-SIT). A digital compensation filter for acceleration-induced effects is designed on the basis of this model. Experimental results explain that the acceleration-induced effects of the pressure sensor were less than 11% after using the digital compensation filter. A series of test data verify the accuracy, reliability, and generality of the model.